publication . Article . Other literature type . 2010

Fast and accurate long-read alignment with Burrows–Wheeler transform

Li, Heng; Durbin, Richard;
Open Access
  • Published: 15 Jan 2010 Journal: Bioinformatics, volume 26, pages 589-595 (issn: 1367-4803, eissn: 1460-2059, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for reads >200 bp because the algorithms are heavily and specifically tuned for short queries with low sequencing error rate. However, some sequencing platforms already produce longer reads and others are expected to become available soon. For longer reads, hashing-based software such as BLAT and SSAHA2 remain the only choices. Nonetheless, these methods are substantially slower than short-read aligners in terms of aligned bases per unit time. Results: We des...
Subjects
free text keywords: Original Papers, Sequence Analysis
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